Genetics and archaeogenetics of South Asia
Genetics and archaeogenetics of South Asia is the study of the genetics and archaeogenetics of the ethnic groups of South Asia. It aims at uncovering these groups' genetic history. The geographic position of South Asia makes its biodiversity important for the study of the early dispersal of anatomically modern humans across Asia.
Studies based on Mitochondrial DNA (mtDNA) variations have reported genetic unity across various South Asian sub–populations. Conclusions of studies based on Y Chromosome variation and Autosomal DNA variation have been varied, although many researchers argue that most of the ancestral nodes of the phylogenetic tree of all the mtDNA types originated in South Asia. Recent genome studies appear to show that most South Asians are descendants of two major ancestral components, one restricted to South Asia (Ancestral South Indian, deriving from IVC-people and a native South Asian population possibly distantly related to the Andamanese) and the other component (Ancestral North Indian) derived from IVC-people and Steppe-people, making it more closely related to those in Central Asia, West Asia and Europe. Genomic studies have described the genetic landscape of South Asia as a composite of West Eurasian and East Asian exogenous components that mixed with the indigenous South Asian groups to create modern-day South Asians. The East Asian ancestry component detected in South Asia is mainly restricted to specific populations in the Himalayan foothills and northeastern part of India.
It has been found that the ancestral node of the phylogenetic tree of all the mtDNA types (mitochondrial DNA haplogroups) typically found in Central Asia, the West Asia and Europe are also to be found in South Asia at relatively high frequencies. The inferred divergence of this common ancestral node is estimated to have occurred slightly less than 50,000 years ago. In India, the major maternal lineages are various M subclades, followed by R and U sublineages. These mitochondrial haplogroups' coalescence times have been approximated to date to 50,000 BP.
The major paternal lineages represented by Y chromosomes are haplogroups R1a1, R2, H, L and J2. Some researchers have argued that Y-DNA Haplogroup R1a1 (M17) is of autochthonous South Asian origin. However, proposals for a Central Asian origin for R1a1 are also quite common.
All the mtDNA and Y-chromosome lineages outside Africa descend from three founder lineages:
All these six founder haplogroups can be found in the present day populations of South Asia. Moreover, the mtDNA haplogroup M and the Y-chromosome haplogroups C and D are restricted to the area east of South Asia. All the West Eurasian populations derive from the N and R haplogroups of mtDNA and the F haplogroup of the Y-chromosome.
Endicott et al. state that these facts are consistent with the hypothesis of a single exodus from East Africa 65,000 years ago via a southern coastal route, with the West Eurasian lineages separating from the South Asian lineages somewhere between East/Northeast Africa and South Asia.
Arguing for the longer term "rival Y-Chromosome model", Stephen Oppenheimer believes that it is highly suggestive that India is the origin of the Eurasian mtDNA haplogroups which he calls the "Eurasian Eves". According to Oppenheimer it is highly probable that nearly all human maternal lineages in Central Asia, the Middle East and Europe descended from only four mtDNA lines that originated in South Asia 50,000–100,000 years ago.
The M macrohaplotype in India includes many subgroups that differ profoundly from other sublineages in East Asia especially Mongoloid populations. The deep roots of M phylogeny clearly ascertain the relic of South Asian lineages as compared to other M sub lineages (in East Asia and elsewhere) suggesting 'in-situ' origin of these sub-haplogroups in South Asia, most likely in India. These deep rooting lineages are not language specific and spread over all the language groups in India.
Virtually all modern Central Asian MtDNA M lineages seem to belong to the Eastern Eurasian (Mongolian) rather than the South Asian subtypes of haplogroup M, which indicates that no large-scale migration from the present Turkic-speaking populations of Central Asia occurred to India. The absence of haplogroup M in Europeans, compared to its equally high frequency among South Asians, East Asians and in some Central Asian populations contrasts with the Western Eurasian leanings of South Asian paternal lineages.
Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans.
The macrohaplogroup R (a very large and old subdivision of macrohaplogroup N) is also widely represented and accounts for the other 40% of South Asian MtDNA. A very old and most important subdivision of it is haplogroup U that, while also present in West Eurasia, has several subclades specific to South Asia.
Haplogroup U is a sub-haplogroup of macrohaplogroup R. The distribution of haplogroup U is a mirror image of that for haplogroup M: the former has not been described so far among eastern Asians but is frequent in European populations as well as among South Asians. South Asian U lineages differ substantially from those in Europe and their coalescence to a common ancestor also dates back to about 50,000 years.
Haplogroup H (Y-DNA) is found at a high frequency in South Asia. H is today rarely found outside of the South Asia but is common among the Romanis, particularly the H-M82 subgroup. H was also quite common in ancient samples of Europe and is still found today at a low frequency in Europeans and Arabs of the Levant. Haplogroup H is frequently found among populations of India, Sri Lanka, Nepal, Pakistan and the Maldives. All three branches of Haplogroup H (Y-DNA) are found in South Asia.
It is a branch of Haplogroup F and descends from GHIJK family. Haplogroup H is believed to have arisen in South Asia between 30,000 and 40,000 years ago. Its probable site of introduction is South Asia, since it is concentrated there. It seems to represent the main Y-Chromosome haplogroup of the paleolithic inhabitants of South Asia. Some individuals in South Asia have also been shown to belong to the much rarer subclade H3 (Z5857). Haplogroup H is by no means restricted to specific populations. For example, H is possessed by about 28.8% of Indo-Aryan castes. and in tribals about 25–35%.
Haplogroup J2 reflects presence from neolithic period in South Asia. The frequency of J2 is higher among a few South Indian castes (19% to 34%) than in North Indian castes (11% to 27%) which are higher in overall actual numbers or Pakistan (12% to 24%). Haplogroup J2 frequency is higher south Indian middle castes at 21%, followed by upper castes at 18.6%, and lower castes 14%. Among caste groups, the highest frequency of J2-M172 was observed among Tamil Vellalar's of South India, at 38.7%. J2 is present in tribals too and has a frequency of 11% in Austro-Asiatic tribals. Among the Austro-Asiatic tribals, the predominant J2 occurs in the Lodha (35%). J2 is also present in the South Indian hill tribe Toda at 38.46%, in the Andh tribe of Telangana at 35.19% and in the Kol tribe of Uttar Pradesh at a frequency of 33.34%. Haplogroup J-P209 was found to be more common in India's Shia Muslims, of which 28.7% belong to haplogroup J, with 13.7% in J-M410, 10.6% in J-M267 and 4.4% in J2b (Eaaswarkhanth 2009).
In Pakistan, the highest frequencies of J2-M172 were observed among the Parsis at 38.89%, the Dravidian speaking Brahuis at 28.18% and the Makrani Balochs at 24%. It also occurs at 18.18% in Makrani Siddis and at 3% in Karnataka Siddis.
Overall, in India J2 is found at a much higher overall frequency in North India than the South. J2-M172 is found at an overall frequency of 10.3% among the Sinhalese people of Sri Lanka. In Maldives, 22% of Maldivian population were found to be haplogroup J2 positive.
According to Dr. Spencer Wells, L-M20 originated in the Pamir Knot region in Tajikistan and migrated into Pakistan and India ca. 30,000 years ago. However, most other studies have proposed a West Asian origin for L-M20 and associated its expansion in the Indus valley (~7,000 YBP) to neolithic farmers. There are three subbranches of haplogroup L: L1-M76 (L1a1), L2-M317 (L1b) and L3-M357 (L1a2), found at varying levels in South Asia.
Haplogroup L shows time of neolithic expansion. The clade is present in the Indian population at an overall frequency of ca.7–15%. Haplogroup L has higher frequency among south Indian castes (ca. 17–19%) and reaches up to 68% in some castes in Karnataka but is somewhat rarer in north Indian castes (ca. 5–6%). The presence of haplogroup L is quite rare among tribal groups (ca. 5,6–7%), however a moderate, 14.6% has been observed among the Chenchus.
In Pakistan, L1-M76 and L3-M357 subclades of L-M20 reaches overall frequencies of 5.1% and 6.8%, respectively. Haplogroup L3 (M357) is found frequently among Burusho (approx. 12%) and Pashtuns (approx. 7%). Its highest frequency can be found in south western Balochistan province along the Makran coast (28%) to Indus River delta. L3a (PK3) is found in approximately 23% of Nuristani in northwest Pakistan.
In South Asia, R1a1 has been observed often with high frequency in a number of demographic groups, as well as with highest STR diversity which lead some to see it as the locus of origin.
While R1a originated ca. 22,000 to 25,000 years ago, its subclade M417 (R1a1a1) diversified ca. 5,800 years ago. The distribution of M417-subclades R1-Z282 (including R1-Z280) in Central- and Eastern Europe and R1-Z93 in Asia suggests that R1a1a diversified within the Eurasian Steppes or the Middle East and Caucasus region. The place of origin of these subclades plays a role in the debate about the origins of Indo-Europeans.
In India, high percentage of this haplogroup is observed in West Bengal Brahmins (72%) to the east, Gujarat Lohanas (60%) to the west, Khatris (67%) in north, Iyengar Brahmins (31%) in the south. It has also been found in several South Indian Dravidian-speaking tribals including the Kotas (41%) of Tamil Nadu Chenchu (26%) and Valmikis of Andhra Pradesh as well as the Yadav and Kallar of Tamil Nadu suggesting that M17 is widespread in these Southern Indians tribes. Besides these, studies show high percentages in regionally diverse groups such as Manipuris (50%)  to the extreme North East and in among Punjabis (47%) to the extreme North West.
In South Asia, the frequency of R2 and R2a lineage is around 10–15% in India and Sri Lanka and 7–8% in Pakistan. At least 90% of R-M124 individuals are located in South Asia. It is also reported in Caucasus and Central Asia at lower frequency. A genetic study by Mondal et al. 2017 concluded that haplogroup Haplogroup R2 originated in northern India and was already present before the Steppe migration.
Among regional groups, it is found among West Bengalis (23%), New Delhi Hindus (20%), Punjabis (5%) and Gujaratis (3%). Among tribal groups, Karmalis of West Bengal showed highest at 100% followed by Lodhas (43%) to the east, while Bhil of Gujarat in the west were at 18%, Tharus of north showed it at 17%, Chenchu and Pallan of south were at 20% and 14% respectively. Among caste groups, high percentages are shown by Jaunpur Kshatriyas (87%), Kamma Chaudhary (73%), Bihar Yadav (50%), Khandayat (46%)and Kallar (44%).
It is also significantly high in many Brahmin groups including Punjabi Brahmins (25%), Bengali Brahmins (22%), Konkanastha Brahmins (20%), Chaturvedis (32%), Bhargavas (32%), Kashmiri Pandits (14%) and Lingayat Brahmins (30%).
North Indian Muslims have a frequency of 19% (Sunni) and 13% (Shia), while Dawoodi Bohra Muslim in the western state of Gujarat have a frequency of 16% and Mappila Muslims of South India have a frequency of 5%.
The R2 haplogroup is found in 14% of the Burusho people. Among the Hunza people it is found at 18% while the Parsis show it at 20%. It is also found in the northeastern part of Afghanistan.
The Indian Genome Variation Consortium (2008), divides the population of South Asia into four ethnolinguistic groups: Indo-European, Dravidian, Tibeto-Burman and Austro-Asiatic. The molecular anthropology studies use three different type of markers: Mitochondrial DNA (mtDNA) variation which is maternally inherited and highly polymorphic, Y Chromosome variation which involves uniparental transmission along the male lines, and Autosomal DNA variation.:04
Most of the studies based on mtDNA variation have reported genetic unity of South Asian populations across language, caste and tribal groups. It is likely that haplogroup M was brought to Asia from East Africa along the southern route by earliest migration wave 78,000 years ago.
According to Kivisild et al. (1999), "Minor overlaps with lineages described in other Eurasian populations clearly demonstrate that recent immigrations have had very little impact on the innate structure of the maternal gene pool of South Asians. Despite the variations found within India, these populations stem from a limited number of founder lineages. These lineages were most likely introduced to South Asia during the Middle Palaeolithic, before the peopling of Europe 48,000 years ago and perhaps the Old World in general." Basu et al. (2003) also emphasises underlying unity of female lineages in India.
Conclusions based on Y Chromosome variation have been more varied than those based on mtDNA variation. While Kivisild et al. (2003) proposes an ancient and shared genetic heritage of male lineages in South Asia, Bamshad et al. (2001) suggests an affinity between South Asian male lineages and west Eurasians proportionate to upper caste rank and places upper caste populations of southern Indian states closer to East Europeans.
Basu et al. (2003) concludes that Austro–Asiatic tribal populations entered India first from the Northwest corridor and much later some of them through Northeastern corridor. Whereas, Kumar et al. (2007) analysed 25 South Asian Austro-Asiatic tribes and found strong paternal genetic link among the sub-linguistic groups of the South Asian Austro-Asiatic populations. Mukherjee et al. (2001) places Pakistanis and North Indians between west Asian and Central Asian populations, whereas Cordaux et al. (2004) argues that the Indian caste populations are closer to Central Asian populations. Sahoo et al. (2006) and Sengupata et al. (2006) suggest that Indian caste populations have not been subject to any recent admixtures. Sanghamitra Sahoo concludes his study with:
It is not necessary, based on the current evidence, to look beyond South Asia for the origins of the paternal heritage of the majority of Indians at the time of the onset of settled agriculture. The perennial concept of people, language, and agriculture arriving to India together through the northwest corridor does not hold up to close scrutiny. Recent claims for a linkage of haplogroups J2, L, R1a, and R2 with a contemporaneous origin for the majority of the Indian castes’ paternal lineages from outside the South Asia are rejected, although our findings do support a local origin of haplogroups F* and H. Of the others, only J2 indicates an unambiguous recent external contribution, from West Asia rather than Central Asia. The current distributions of haplogroup frequencies are, with the exception of the lineages, predominantly driven by geographical, rather than cultural determinants. Ironically, it is in the northeast of India, among the TB groups that there is clear-cut evidence for large-scale demic diffusion traceable by genes, culture, and language, but apparently not by agriculture.
Closest neighbor analysis done by Mondal et al. 2017 concluded that Indian Y-lineages are close to southern European populations and the time of divergence between the two predated Steppe migration.":
These results suggest that the European-related ancestry in Indian populations might be much older and more complex than anticipated, and might originate from the ﬁrst wave of agriculturists or even earlier
Results of studies based upon autosomal DNA variation have also been varied. In a major study (2009) using over 500,000 biallelic autosomal markers, Reich hypothesized that the modern South Asian population was the result of admixture between two genetically divergent ancestral populations dating from the post-Holocene era. These two "reconstructed" ancient populations he termed "Ancestral South Indians" (ASI) and "Ancestral North Indians" (ANI). According to Reich: "ANI ancestry is significantly higher in Indo-European than Dravidian speakers, suggesting that the ancestral ASI may have spoken a Dravidian language before mixing with the ANI." While the ANI is genetically close to Middle Easterners, Central Asians and Europeans, the ASI is not closely related to groups outside of the subcontinent. As no "ASI" ancient DNA is available, the indigenous Andamanese Onge are used as an (imperfect) proxy of ASI, though nevertheless distinct from (according to Reich et al., the Andamanese, though distinct from them, are the closest living population to ASI). According to Reich et al., both ANI and ASI ancestry are found all over the subcontinent (in both northern and southern India) in varying proportions, and that “ANI ancestry ranges from 39-71% in India, and is higher in traditionally upper caste and Indo-European speakers."
Moorjani et al. 2013 state that the ASI, though not closely related to any living group, are "related (distantly) to indigenous Andaman Islanders." Moorjani et al. also suggest possible gene flow into the Andamanese from a population related to the ASI. The study concluded that “almost all groups speaking Indo-European or Dravidian languages lie along a gradient of varying relatedness to West Eurasians in PCA (referred to as “Indian cline”)”.
A 2013 study using the single-nucleotide polymorphism (SNP), shows that the genome of Andamanese people (Onge) is closer to those of other Oceanic Negrito groups than to that of South Asians.
According to Basu et al. 2016, further analysis revealed that the genomic structure of mainland Indian populations is best explained by contributions from four ancestral components. In addition to the ANI and ASI, Basu et. al (2016) identified two ancestral components in mainland India that are major for the Austro-Asiatic-speaking tribals and the Tibeto-Burman speakers, which they denoted as AAA (for “Ancestral Austro-Asiatic”) and ATB (for "Ancestral Tibeto-Burman") respectively. The study also infers that the populations of the Andaman Islands archipelago form a distinct ancestry, which "was found to be coancestral to Oceanic populations".
The cline of admixture between the ANI and ASI lineages is dated to the period of c. 4.2–1.9 kya by Moorjani et al. (2013), corresponding to the Indian Bronze Age, and associated by the authors with the process of deurbanisation of the Indus Valley Civilization and the population shift to the Gangetic system in the incipient Indian Iron Age. Basu et al. (2003) suggests that "Dravidian tribals were possibly widespread throughout India before the arrival of the Indo-European-speaking nomads" and that "formation of populations by fission that resulted in founder and drift effects have left their imprints on the genetic structures of contemporary populations". The geneticist PP Majumder (2010) has recently argued that the findings of Reich et al. (2009) are in remarkable concordance with previous research using mtDNA and Y-DNA:
Central Asian populations are supposed to have been major contributors to the Indian gene pool, particularly to the northern Indian gene pool, and the migrants had supposedly moved into India through what is now Afghanistan and Pakistan. Using mitochondrial DNA variation data collated from various studies, we have shown that populations of Central Asia and Pakistan show the lowest coefficient of genetic differentiation with the north Indian populations, a higher differentiation with the south Indian populations, and the highest with the northeast Indian populations. Northern Indian populations are genetically closer to Central Asians than populations of other geographical regions of India... . Consistent with the above findings, a recent study using over 500,000 biallelic autosomal markers has found a north to south gradient of genetic proximity of Indian populations to western Eurasians. This feature is likely related to the proportions of ancestry derived from the western Eurasian gene pool, which, as this study has shown, is greater in populations inhabiting northern India than those inhabiting southern India.
Chaubey et al. 2015 detected a distinctive East Asian ancestral component, mainly restricted to specific populations in the foothills of Himalaya and northeastern part of India. Highest frequency of the component is observed among the Tibeto-Burmese speaking groups of northeast and is also detected at high levels in Andamanese populations, with substantial presence among Austroasiatic speakers. It is found to be largely absent in Indo-European and Dravidian speakers, except in some specific ethnic groups living in the Himalayan foothills and central-south India. The researchers however suggested that the Han ancestry (proxy for East Asians) measured in the studied Andamanese groups is because of partial capture of the affinity of the Andamanese with Melanesians and Malaysian Negritos, as a previous study by Chaubey et al. suggested "a deep common ancestry" between Andamanese, Melanesians and other Negrito groups (as well as South Asians), and an affinity between Southeast Asian Negritos and Melanesians (as well as the Andamanese) with East Asians.
Lazaridis et al. (2016) notes "The demographic impact of steppe related populations on South Asia was substantial, as the Mala, a south Indian Dalit population with minimal Ancestral North Indian (ANI) along the 'Indian Cline' of such ancestry is inferred to have ~ 18 % steppe-related ancestry, while the Kalash of Pakistan are inferred to have ~ 50 % steppe-related ancestry." Lazaridis et al.'s 2016 study estimated (6.5–50.2 %) steppe related admixture in South Asians. Lazaridis et al. further notes that "A useful direction of future research is a more comprehensive sampling of ancient DNA from steppe populations, as well as populations of central Asia (east of Iran and south of the steppe), which may reveal more proximate sources of the ANI than the ones considered here, and of South Asia to determine the trajectory of population change in the area directly.
Pathak et al. 2018 concluded that the Indo-European speakers of Gangetic Plains and the Dravidian speakers have significant Yamnaya Early-Middle Bronze Age (Steppe_EMBA) ancestry but no Middle-Late Bronze Age Steppe (Steppe_MLBA) ancestry. On the other hand, the "North-Western Indian and Pakistani" populations (PNWI) showed significant Steppe_MLBA ancestry along with Yamnaya (Steppe_EMBA) ancestry. The study also noted that ancient South Asian samples had significantly higher Steppe_MLBA than Steppe_EMBA (or Yamnaya). The study also suggested that the Rors could be used as a proxy for the ANI.
David Reich in his 2018 book Who We Are and How We Got Here states that the 2016 analyses found the ASI to have large amounts of an ancestry component deriving from Iranian farmers (about 25% of their ancestry), with the remaining 75% of their ancestry deriving from native South Asian hunter-gatherers. He adds that ASI were unlikely the local hunter-gatherers of South Asia as previously established, but a population responsible for spreading agriculture throughout South Asia. In the case of the ANI, the Iranian farmer ancestry is 50%, with the rest being from steppe groups related to the Yamnaya.
Narasimhan et al. (2018), similarly, conclude that ANI and ASI were formed in the 2nd millennium BCE. They were preceded by a mixture of AASI (ancient ancestral south Indian, i.e. hunter-gatherers sharing a common root with the Andamanese); and Iranian agriculturalists who arrived in India ca. 4700–3000 BCE, and "must have reached the Indus Valley by the 4th millennium BCE". According to Narasimhan et al., this mixed population, which probably was native to the Indus Valley Civilisation, "contributed in large proportions to both the ANI and ASI", which took shape during the 2nd millennium BCE. ANI formed out of a mixture of "Indus Periphery-related groups" and migrants from the steppe, while ASI was formed out of "Indus Periphery-related groups" who moved south and mixed further with local hunter-gatherers. The ancestry of the ASI population is suggested to have averaged about 73% from the AASI and 27% from Iranian-related farmers. Narasimhan et al. observe that samples from the Indus periphery group are always mixes of the same two proximal sources of AASI and Iranian agriculturalist-related ancestry; with "one of the Indus Periphery individuals having ~42% AASI ancestry and the other two individuals having ~14-18% AASI ancestry" (with the remainder of their ancestry being from the Iranian agriculturalist-related population).
A genetic study by Yelmen et al. (2019) shows that modern South Asian populations are generally closest to West-Eurasians. They concluded that modern South Asians are basically a mixture of a native South Asian genetic component and a later-arriving West-Eurasian component (derived from both West Asia and the western Steppes). The authors also argue that the native South Asian genetic component is distinct from the Andamanese, and that the Andamanese are thus an imperfect proxy. The Andamanese component (represented by the Andamanese Onge) was not found in the northern Indian Gujarati, and thus it is suggested that the South Indian tribal Paniya people would serve as a better proxy than the Andamanese (Onge) for the "native South Asian" component in modern South Asians.
Two genetic studies (Shinde et al. 2019 and Narasimhan et al. 2019,) analysing remains from the Indus Valley civilisation (of parts of Bronze Age Northwest India and East Pakistan), found them to have a mixture of ancestry: Shinde et al. found their samples to have about 50-98% of their genome from peoples related to early Iranian farmers, and from 2-50% of their genome from native South Asian hunter-gatherers sharing a common ancestry with the Andamanese, with the Iranian-related ancestry being on average predominant. The samples analyzed by Narasimhan et al. had 45–82% Iranian farmer-related ancestry and 11–50% AASI (or Andamanese-related hunter-gatherer ancestry). The analysed samples of both studies have little to none of the "Steppe ancestry" component associated with later Indo-European migrations into India. The authors found that the respective amounts of those ancestries varied significantly between individuals, and concluded that more samples are needed to get the full picture of Indian population history.
Studies by Watkins et al. (2005) and Kivisild et al. (2003) based on autosomal markers conclude that Indian caste and tribal populations have a common ancestry. Reddy et al. (2005) found fairly uniform allele frequency distributions across caste groups of southern Andhra Pradesh, but significantly larger genetic distance between caste groups and tribes indicating genetic isolation of the tribes and castes.
Viswanathan et al. (2004) in a study on genetic structure and affinities among tribal populations of southern India concludes, " Otherwise, analyses of population relationships showed that all Indian and South Asian populations are still similar to one another, regardless of phenotypic characteristics, and do not show any particular affinities to Africans. We conclude that the phenotypic similarities of some Indian groups to Africans do not reflect a close relationship between these groups, but are better explained by convergence."Genetic differentiation was high and genetic distances were not significantly correlated with geographic distances. Genetic drift therefore probably played a significant role in shaping the patterns of genetic variation observed in southern Indian tribal populations.
A 2011 study published in the American Journal of Human Genetics indicates that Indian ancestral components are the result of a more complex demographic history than was previously thought. According to the researchers, South Asia harbours two major ancestral components, one of which is spread at comparable frequency and genetic diversity in populations of Central Asia, West Asia and Europe; the other component is more restricted to South Asia. However, if one were to rule out the possibility of a large-scale Indo-Aryan migration, these findings suggest that the genetic affinities of both Indian ancestral components are the result of multiple gene flows over the course of thousands of years.